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(conjugation / ATPase / Archaea / molecular key / Walker
box)
Edited by John Mekalanos, Harvard Medical School, Boston, MA, and
approved January 2, 2001 (received for review September 11, 2000)
Macromolecular transport systems in bacteria currently are
classified by function and sequence comparisons into five basic types.
In this classification system, type II and type IV secretion systems
both possess members of a superfamily of genes for putative NTP
hydrolase (NTPase) proteins that are strikingly similar in structure,
function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB,
PilT, and ComG1. The predicted protein product of tadA,
a recently discovered gene required for tenacious adherence of
Actinobacillus actinomycetemcomitans, also has
significant sequence similarity to members of this superfamily and to
several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and
tadA-like genes to those encoding the putative NTPases
of type II/IV secretion, we used a phylogenetic approach to obtain a
genealogy of 148 NTPase genes and reconstruct a scenario of gene
superfamily evolution. In this phylogeny, clear distinctions can be
made between type II and type IV families and their constituent
subfamilies. In addition, the subgroup containing tadA
constitutes a novel and extremely widespread subfamily of the family
encompassing all putative NTPases of type IV secretion systems. We
report diagnostic amino acid residue positions for each major
monophyletic family and subfamily in the phylogenetic tree, and we
propose an easy method for precisely classifying and naming putative
NTPase genes based on phylogeny. This molecular key-based method can be
applied to other gene superfamilies and represents a valuable tool for genome analysis.
Evolution
Phylogeny of genes for secretion NTPases: Identification of the
widespread tadA subfamily and development of a diagnostic key for gene classification
,,
,§, and
Department of Microbiology, College of Physicians and
Surgeons, Columbia University, New York, NY 10032; and
Molecular Laboratories, American Museum of Natural
History, New York, NY 10024
§
To whom reprint requests should be addressed at:
Molecular Laboratories, American Museum of Natural History, Central
Park West and 79th Street, New York, NY 10024. E-mail:
desalle{at}amnh.org.
www.pnas.org/cgi/doi/10.1073/pnas.051436598
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